OTTAWA — The Harper government is going to have to decide whether resupplying Canada’s navy or Arctic sovereignty is more important thanks to a looming collision at a Vancouver shipyard.

The Royal Canadian Navy is designing new joint support ships to replace its 50-year-old resupply vessels, which were supposed to have been retired in 2012 and have become environmentally unsound and prohibitively expensive to maintain.

The Canadian Coast Guard is also designing a new polar-class icebreaker, the CCGS John G. Diefenbaker, to replace its existing heavy icebreaker, the Louis S. St-Laurent, which is due to be retired in 2017.

But while both are expected to be ready for construction at the same time, the Vancouver shipyard slated to build them can only handle one project at a time.

This scheduling conflict was acknowledged in a recent Defence Department report tabled in Parliament, which noted that “the Joint Support Ship and the Polar Icebreaker are progressing on a very similar schedule such that they both could be ready for construction at the same time.”

The report goes on to say the first joint support ship will be delivered around by 2018, “assuming JSS is not delayed by the initial Coast Guard projects and the Polar Icebreaker program.”

Any delay in replacing the navy’s existing resupply vessels could be potentially devastating for the maritime fleet because new ships are needed immediately, while delays undercut the purchasing power of the $2.6 billion set aside for the project.

This was underscored by a Parliamentary Budget Office report in March that found it could cost as much as $4.13 billion to replace the resupply ships and not $2.6 billion, in large part because of delays already incurred.

Yet delaying construction of the $800-million John G. Diefenbaker could cause its own problems as it could leave the Coast Guard without significant icebreaking capabilities as the Louis St-Laurent is already slated to be decommissioned before the Diefenbaker comes online.

Deciding which project has priority will likely be a political decision — and the government has not yet figured out how to address the competing timelines.

“A decision has not yet been made,” Public Works spokeswoman Lucie Brosseau said in an email. “The (National Shipbuilding Procurement Strategy) secretariat, working together with the Department of National Defence and Canadian Coast Guard, is currently developing the framework for the sequencing decision for the JSS and the Polar Icebreaker projects.”

Vancouver shipbuilder Seaspan Marine, which owns the shipyards where the vessels will be built, did not respond to inquiries.

Conference of Defence Association analyst David Perry said the government faces a tough decision as the navy needs new resupply ships and the Coast Guard needs a new icebreaker.

“The navy needs to get new supply ships ASAP,” Perry said. “But on the other hand our icebreakers were built many, many decades ago.

“They’re basically going to have to decide whether they want to do Arctic operations first, or whether they want to do open-ocean naval operations first,” he added. “They need both and there’s no easy choice.”

The pending conflict is yet the latest issue facing the $35-billion national shipbuilding strategy, which the Harper government has been holding up as an unmitigated success against a backdrop of problems related to the F-35, search-and-rescue airplanes and other military procurement projects.